Publications

Publication library

GRDI-AMR.com maintains a publicly-available library of publications related to the GRDI-AMR1|2 projects. For more information, see the publication library documentation.

The library is compiled on a best-effort basis and may be incomplete.

Import the publication library:

Last update: 2024.07.02

GRDI-AMR1

Adator, E. H., Narvaez-Bravo, C., Zaheer, R., Cook, S. R., Tymensen, L., Hannon, S. J., Booker, C. W., Church, D., Read, R. R., & McAllister, T. A. (2020). A One Health Comparative Assessment of Antimicrobial Resistance in Generic and Extended-Spectrum Cephalosporin-Resistant Escherichia coli from Beef Production, Sewage and Clinical Settings. Microorganisms, 8(6), 885. https://doi.org/10.3390/microorganisms8060885

Adator, E. H., Walker, M., Narvaez-Bravo, C., Zaheer, R., Goji, N., Cook, S. R., Tymensen, L., Hannon, S. J., Church, D., Booker, C. W., Amoako, K., Nadon, C. A., Read, R., & McAllister, T. A. (2020). Whole Genome Sequencing Differentiates Presumptive Extended Spectrum Beta-Lactamase Producing Escherichia coli along Segments of the One Health Continuum. Microorganisms, 8(3), 448. https://doi.org/10.3390/microorganisms8030448

Ben Said, L., Emond‐Rheault, J., Soltani, S., Telhig, S., Zirah, S., Rebuffat, S., Diarra, M. S., Goodridge, L., Levesque, R. C., & Fliss, I. (2020). Phenomic and genomic approaches to studying the inhibition of multiresistant Salmonella enterica by microcin J25. Environmental Microbiology, 22(7), 2907–2920. https://doi.org/10.1111/1462-2920.15045

Boyd, D. A., Lefebvre, B., Mataseje, L. F., Gagnon, S., Roger, M., Savard, P., Longtin, J., & Mulvey, M. R. (2020). Enterobacter sp. N18-03635 harbouring blaFRI-6 class A carbapenemase, Canada. Journal of Antimicrobial Chemotherapy, 75(2), 486–488. https://doi.org/10.1093/jac/dkz438

Boyd, D. A., Lisboa, L. F., Rennie, R., Zhanel, G. G., Dingle, T. C., & Mulvey, M. R. (2019). Identification of a novel metallo-β-lactamase, CAM-1, in clinical Pseudomonas aeruginosa isolates from Canada. Journal of Antimicrobial Chemotherapy, 74(6), 1563–1567. https://doi.org/10.1093/jac/dkz066

Boyd, D. A., Mataseje, L. F., Pelude, L., Mitchell, R., Bryce, E., Roscoe, D., Embree, J., Katz, K., Kibsey, P., Lavallee, C., Simor, A. E., Taylor, G., Turgeon, N., Langley, J. M., Amaratunga, K., Mulvey, M. R., Canadian Nosocomial Infection Surveillance Program, Wong, A., McGeer, A., … Longtin, Y. (2019). Results from the Canadian Nosocomial Infection Surveillance Program for detection of carbapenemase-producing Acinetobacter spp. In Canadian hospitals, 2010–16. Journal of Antimicrobial Chemotherapy, 74(2), 315–320. https://doi.org/10.1093/jac/dky416

Carson, C., Li, X.-Z., Agunos, A., Loest, D., Chapman, B., Finley, R., Mehrotra, M., Sherk, L. M., Gaumond, R., & Irwin, R. (2019). Ceftiofur-resistant Salmonella enterica serovar Heidelberg of poultry origin – a risk profile using the Codex framework. Epidemiology and Infection, 147, e296. https://doi.org/10.1017/S0950268819001778

Collineau, L., Boerlin, P., Carson, C. A., Chapman, B., Fazil, A., Hetman, B., McEwen, S. A., Parmley, E. J., Reid-Smith, R. J., Taboada, E. N., & Smith, B. A. (2019). Integrating Whole-Genome Sequencing Data Into Quantitative Risk Assessment of Foodborne Antimicrobial Resistance: A Review of Opportunities and Challenges. Frontiers in Microbiology, 10, 1107. https://doi.org/10.3389/fmicb.2019.01107

Collineau, L., Chapman, B., Bao, X., Sivapathasundaram, B., Carson, C. A., Fazil, A., Reid-Smith, R. J., & Smith, B. A. (2020). A farm-to-fork quantitative risk assessment model for Salmonella Heidelberg resistant to third-generation cephalosporins in broiler chickens in Canada. International Journal of Food Microbiology, 330, 108559. https://doi.org/10.1016/j.ijfoodmicro.2020.108559

Collineau, L., Phillips, C., Chapman, B., Agunos, A., Carson, C., Fazil, A., Reid-Smith, R. J., & Smith, B. A. (2020). A within-flock model of Salmonella Heidelberg transmission in broiler chickens. Preventive Veterinary Medicine, 174, 104823. https://doi.org/10.1016/j.prevetmed.2019.104823

Cooper, A. L., Carrillo, C. D., DeschêNes, M., & Blais, B. W. (2021). Genomic Markers for Quaternary Ammonium Compound Resistance as a Persistence Indicator for Listeria monocytogenes Contamination in Food Manufacturing Environments. Journal of Food Protection, 84(3), 389–398. https://doi.org/10.4315/JFP-20-328

Cooper, A. L., Carter, C., McLeod, H., Wright, M., Sritharan, P., Tamber, S., Wong, A., Carrillo, C. D., & Blais, B. W. (2021). Detection of carbapenem-resistance genes in bacteria isolated from wastewater in Ontario. FACETS, 6(1), 569–591. https://doi.org/10.1139/facets-2020-0101

Cooper, A. L., Low, A. J., Koziol, A. G., Thomas, M. C., Leclair, D., Tamber, S., Wong, A., Blais, B. W., & Carrillo, C. D. (2020). Systematic Evaluation of Whole Genome Sequence-Based Predictions of Salmonella Serotype and Antimicrobial Resistance. Frontiers in Microbiology, 11, 549. https://doi.org/10.3389/fmicb.2020.00549

Das, Q., Islam, Md. R., Lepp, D., Tang, J., Yin, X., Mats, L., Liu, H., Ross, K., Kennes, Y. M., Yacini, H., Warriner, K., Marcone, M. F., & Diarra, M. S. (2020a). Corrigendum: Gut Microbiota, Blood Metabolites, and Spleen Immunity in Broiler Chickens Fed Berry Pomaces and Phenolic-Enriched Extractives. Frontiers in Veterinary Science, 7, 541. https://doi.org/10.3389/fvets.2020.00541

Das, Q., Islam, Md. R., Lepp, D., Tang, J., Yin, X., Mats, L., Liu, H., Ross, K., Kennes, Y. M., Yacini, H., Warriner, K., Marcone, M. F., & Diarra, M. S. (2020b). Gut Microbiota, Blood Metabolites, and Spleen Immunity in Broiler Chickens Fed Berry Pomaces and Phenolic-Enriched Extractives. Frontiers in Veterinary Science, 7, 150. https://doi.org/10.3389/fvets.2020.00150

Das, Q., Lepp, D., Yin, X., Ross, K., McCallum, J. L., Warriner, K., Marcone, M. F., & Diarra, M. S. (2019). Transcriptional profiling of Salmonella enterica serovar Enteritidis exposed to ethanolic extract of organic cranberry pomace. PLOS ONE, 14(7), e0219163. https://doi.org/10.1371/journal.pone.0219163

Das, Q., Tang, J., Yin, X., Ross, K., Warriner, K., Marcone, M. F., & Diarra, M. S. (2021). Organic cranberry pomace and its ethanolic extractives as feed supplement in broiler: Impacts on serum Ig titers, liver and bursal immunity. Poultry Science, 100(2), 517–526. https://doi.org/10.1016/j.psj.2020.09.044

Diarra, M. S., Hassan, Y. I., Block, G. S., Drover, J. C. G., Delaquis, P., & Oomah, B. D. (2020). Antibacterial activities of a polyphenolic-rich extract prepared from American cranberry (Vaccinium macrocarpon) fruit pomace against Listeria spp. LWT, 123, 109056. https://doi.org/10.1016/j.lwt.2020.109056

Diarra, M. S., Zhao, X., & Butaye, P. (2021). Editorial: Antimicrobial Use, Antimicrobial Resistance, and the Microbiome in Food Animals. Frontiers in Veterinary Science, 7, 638781. https://doi.org/10.3389/fvets.2020.638781

Eshaghi, A., Zittermann, S., Bharat, A., Mulvey, M. R., Allen, V. G., & Patel, S. N. (2020). Importation of Extensively Drug-Resistant Salmonella enterica Serovar Typhi Cases in Ontario, Canada. Antimicrobial Agents and Chemotherapy, 64(5), e02581-19. https://doi.org/10.1128/AAC.02581-19

Hannon, S. J., Brault, S. A., Otto, S. J. G., Morley, P. S., McAllister, T. A., Booker, C. W., & Gow, S. P. (2020). Feedlot Cattle Antimicrobial Use Surveillance Network: A Canadian Journey. Frontiers in Veterinary Science, 7, 596042. https://doi.org/10.3389/fvets.2020.596042

Holman, D. B., Gzyl, K. E., Zaheer, R., Jones, T. H., & McAllister, T. A. (2019). Draft Genome Sequences of 43 Enterococcus faecalis and Enterococcus faecium Isolates from a Commercial Beef Processing Plant and Retail Ground Beef. Microbiology Resource Announcements, 8(42), e00974-19. https://doi.org/10.1128/MRA.00974-19

Islam, Md. R., Hassan, Y. I., Das, Q., Lepp, D., Hernandez, M., Godfrey, D. V., Orban, S., Ross, K., Delaquis, P., & Diarra, M. S. (2020). Dietary organic cranberry pomace influences multiple blood biochemical parameters and cecal microbiota in pasture-raised broiler chickens. Journal of Functional Foods, 72, 104053. https://doi.org/10.1016/j.jff.2020.104053

Kahn, L. H., Bergeron, G., Bourassa, M. W., De Vegt, B., Gill, J., Gomes, F., Malouin, F., Opengart, K., Ritter, G. D., Singer, R. S., Storrs, C., & Topp, E. (2019). From farm management to bacteriophage therapy: Strategies to reduce antibiotic use in animal agriculture. Annals of the New York Academy of Sciences, 1441(1), 31–39. https://doi.org/10.1111/nyas.14034

Laskey, A., Devenish, J., Kang, M., Savic, M., Chmara, J., Dan, H., Lin, M., Robertson, J., Bessonov, K., Gurnik, S., Liu, K., Nash, J. H. E., Topp, E., & Guan, J. (2021). Mobility of β-lactam resistance under ampicillin treatment in gut microbiota suffering from pre-disturbance. Microbial Genomics, 7(12). https://doi.org/10.1099/mgen.0.000713

Laskey, A., Ottenbrite, M., Devenish, J., Kang, M., Savic, M., Nadin-Davis, S., Chmara, J., Lin, M., Robertson, J., Bessonov, K., Gurnik, S., Liu, K., Nash, J. H. E., Scott, A., Topp, E., & Guan, J. (2020). Mobility of β-Lactam Resistance Under Bacterial Co-infection and Ampicillin Treatment in a Mouse Model. Frontiers in Microbiology, 11, 1591. https://doi.org/10.3389/fmicb.2020.01591

Lau, C. H.-F., DeJong, E. N., Dussault, F., Carrillo, C., Stogios, P. J., Savchenko, A., & Topp, E. (2020). A penicillin-binding protein that can promote advanced-generation cephalosporin resistance and genome adaptation in the opportunistic pathogen Pseudomonas aeruginosa. International Journal of Antimicrobial Agents, 55(3), 105896. https://doi.org/10.1016/j.ijantimicag.2020.105896

Lau, C. H.-F., Tien, Y.-C., Stedtfeld, R. D., & Topp, E. (2020). Impacts of multi-year field exposure of agricultural soil to macrolide antibiotics on the abundance of antibiotic resistance genes and selected mobile genetic elements. Science of The Total Environment, 727, 138520. https://doi.org/10.1016/j.scitotenv.2020.138520

Links, M. G., Dumonceaux, T. J., McCarthy, E. L., Hemmingsen, S. M., Topp, E., & Town, J. R. (2021). CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial Ecosystems. Microorganisms, 9(4), 816. https://doi.org/10.3390/microorganisms9040816

Liu, X., Teixeira, J. S., Ner, S., Ma, K. V., Petronella, N., Banerjee, S., & Ronholm, J. (2020). Exploring the Potential of the Microbiome as a Marker of the Geographic Origin of Fresh Seafood. Frontiers in Microbiology, 11, 696. https://doi.org/10.3389/fmicb.2020.00696

Ma, Y., Chen, J., Fong, K., Nadya, S., Allen, K., Laing, C., Ziebell, K., Topp, E., Carroll, L. M., Wiedmann, M., Delaquis, P., & Wang, S. (2021). Antibiotic Resistance in Shiga Toxigenic Escherichia coli Isolates from Surface Waters and Sediments in a Mixed Use Urban Agricultural Landscape. Antibiotics, 10(3), 237. https://doi.org/10.3390/antibiotics10030237

MacKinnon, M. C., Sargeant, J. M., Pearl, D. L., Reid-Smith, R. J., Carson, C. A., Parmley, E. J., & McEwen, S. A. (2020). Evaluation of the health and healthcare system burden due to antimicrobial-resistant Escherichia coli infections in humans: A systematic review and meta-analysis. Antimicrobial Resistance & Infection Control, 9(1), 200. https://doi.org/10.1186/s13756-020-00863-x

Maguire, F., Rehman, M. A., Carrillo, C., Diarra, M. S., & Beiko, R. G. (2019). Identification of Primary Antimicrobial Resistance Drivers in Agricultural Nontyphoidal Salmonella enterica Serovars by Using Machine Learning. mSystems, 4(4), e00211-19. https://doi.org/10.1128/mSystems.00211-19

Manaia, C. M., Graham, D., Topp, E., Martinez, J. L., Collignon, P., & Gaze, W. H. (2020). Antibiotic Resistance in the Environment: Expert Perspectives. In C. M. Manaia, E. Donner, I. Vaz-Moreira, & P. Hong (Eds.), Antibiotic Resistance in the Environment (Vol. 91, pp. 1–18). Springer International Publishing. https://doi.org/10.1007/698_2020_472

Mangat, C. S., Bekal, S., Avery, B. P., Côté, G., Daignault, D., Doualla-Bell, F., Finley, R., Lefebvre, B., Bharat, A., Parmley, E. J., Reid-Smith, R. J., Longtin, J., Irwin, R. J., Mulvey, M. R., on behalf of the Canadian Integrated Program for Antimicrobial Resistance Surveillance Public Health Partnership, Hoang, L., Louie, M., Romanow, R., Alexander, D. C., … Zahariadis, G. (2019). Genomic Investigation of the Emergence of Invasive Multidrug-Resistant Salmonella enterica Serovar Dublin in Humans and Animals in Canada. Antimicrobial Agents and Chemotherapy, 63(6), e00108-19. https://doi.org/10.1128/AAC.00108-19

Marano, R. B. M., Fernandes, T., Manaia, C. M., Nunes, O., Morrison, D., Berendonk, T. U., Kreuzinger, N., Tenson, T., Corno, G., Fatta-Kassinos, D., Merlin, C., Topp, E., Jurkevitch, E., Henn, L., Scott, A., Heß, S., Slipko, K., Laht, M., Kisand, V., … Cytryn, E. (2020). A global multinational survey of cefotaxime-resistant coliforms in urban wastewater treatment plants. Environment International, 144, 106035. https://doi.org/10.1016/j.envint.2020.106035

Martin-Laurent, F., Topp, E., Billet, L., Batisson, I., Malandain, C., Besse-Hoggan, P., Morin, S., Artigas, J., Bonnineau, C., Kergoat, L., Devers-Lamrani, M., & Pesce, S. (2019). Environmental risk assessment of antibiotics in agroecosystems: Ecotoxicological effects on aquatic microbial communities and dissemination of antimicrobial resistances and antibiotic biodegradation potential along the soil-water continuum. Environmental Science and Pollution Research, 26(18), 18930–18937. https://doi.org/10.1007/s11356-019-05122-0

Mataseje, L. F., Boyd, D. A., Mulvey, M. R., & Longtin, Y. (2019). Two Hypervirulent Klebsiella pneumoniae Isolates Producing a bla _KPC-2 Carbapenemase from a Canadian Patient. Antimicrobial Agents and Chemotherapy, 63(7), e00517-19. https://doi.org/10.1128/AAC.00517-19

McDonald, K. L., Garland, S., Carson, C. A., Gibbens, K., Parmley, E. J., Finley, R., & MacKinnon, M. C. (2021). Measures used to assess the burden of ESBL-producing Escherichia coli infections in humans: A scoping review. JAC-Antimicrobial Resistance, 3(1), dlaa104. https://doi.org/10.1093/jacamr/dlaa104

Petrillo, M., Fabbri, M., Kagkli, D. M., & Querci, M. (2022). A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing [version 2; peer review: 1 approved, 2 approved with reservations].

Petrillo, M., Fabbri, M., Kagkli, D. M., Querci, M., Van Den Eede, G., Alm, E., Aytan-Aktug, D., Capella-Gutierrez, S., Carrillo, C., Cestaro, A., Chan, K.-G., Coque, T., Endrullat, C., Gut, I., Hammer, P., Kay, G. L., Madec, J.-Y., Mather, A. E., McHardy, A. C., … Angers-Loustau, A. (2021). A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing. F1000Research, 10, 80. https://doi.org/10.12688/f1000research.39214.1

Petronella, N., Kundra, P., Auclair, O., Hébert, K., Rao, M., Kingsley, K., De Bruyne, K., Banerjee, S., Gill, A., Pagotto, F., Tamber, S., & Ronholm, J. (2019). Changes detected in the genome sequences of Escherichia coli , Listeria monocytogenes , Vibrio parahaemolyticus , and Salmonella enterica after serial subculturing. Canadian Journal of Microbiology, 65(11), 842–850. https://doi.org/10.1139/cjm-2019-0235

Poulin-Laprade, D., Brouard, J.-S., Gagnon, N., Turcotte, A., Langlois, A., Matte, J. J., Carrillo, C. D., Zaheer, R., McAllister, T. A., Topp, E., & Talbot, G. (2021). Resistance Determinants and Their Genetic Context in Enterobacteria from a Longitudinal Study of Pigs Reared under Various Husbandry Conditions. Applied and Environmental Microbiology, 87(8), e02612-20. https://doi.org/10.1128/AEM.02612-20

Rehman, M. A., Hasted, T.-L., Persaud-Lachhman, M. G., Yin, X., Carrillo, C., & Diarra, M. S. (2019). Genome Analysis and Multiplex PCR Method for the Molecular Detection of Coresistance to Cephalosporins and Fosfomycin in Salmonella enterica Serovar Heidelberg. Journal of Food Protection, 82(11), 1938–1949. https://doi.org/10.4315/0362-028X.JFP-19-205

Rehman, M. A., Rempel, H., Carrillo, C. D., Ziebell, K., Allen, K., Manges, A. R., Topp, E., & Diarra, M. S. (2022). Virulence Genotype and Phenotype of Multiple Antimicrobial-Resistant Escherichia coli Isolates from Broilers Assessed from a “One-Health” Perspective. Journal of Food Protection, 85(2), 336–354. https://doi.org/10.4315/JFP-21-273

Robertson, J., Bessonov, K., Schonfeld, J., & Nash, J. H. E. (2020). Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance. Microbial Genomics, 6(10). https://doi.org/10.1099/mgen.0.000435

Sanderson, H., Ortega-Polo, R., Zaheer, R., Goji, N., Amoako, K. K., Brown, R. S., Majury, A., Liss, S. N., & McAllister, T. A. (2020). Comparative genomics of multidrug-resistant Enterococcus spp. Isolated from wastewater treatment plants. BMC Microbiology, 20(1), 20. https://doi.org/10.1186/s12866-019-1683-4

Schonfeld, J., Clark, C., Robertson, J., Arya, G., Eagle, S. H. C., Gurnik, S., Johnson, R., Labbe, G., Liu, K., Kernaghan, S., Mazzocco, A., MacKinnon, J., Ziebell, K., & Nash, J. H. E. (2021). Complete Genome Sequences for 36 Canadian Salmonella enterica Serovar Typhimurium and I 1,4,[5],12:i:– Isolates from Clinical and Animal Sources. Microbiology Resource Announcements, 10(1), e00734-20. https://doi.org/10.1128/MRA.00734-20

Scott, A., Murray, R., Tien, Y.-C., & Topp, E. (2022). Contamination of hay and haylage with enteric bacteria and selected antibiotic resistance genes following fertilization with dairy manure or biosolids. Canadian Journal of Microbiology, 68(4), 249–257. https://doi.org/10.1139/cjm-2021-0326

Steinkey, R., Moat, J., Gannon, V., Zovoilis, A., & Laing, C. (2020). Application of artificial intelligence to the in silico assessment of antimicrobial resistance and risks to human and animal health presented by priority enteric bacterial pathogens. Canada Communicable Disease Report, 180–185. https://doi.org/10.14745/ccdr.v46i06a05

Subirats, J., Murray, R., Scott, A., Lau, C. H.-F., & Topp, E. (2020). Composting of chicken litter from commercial broiler farms reduces the abundance of viable enteric bacteria, Firmicutes, and selected antibiotic resistance genes. Science of The Total Environment, 746, 141113. https://doi.org/10.1016/j.scitotenv.2020.141113

Subirats, J., Murray, R., Yin, X., Zhang, T., & Topp, E. (2021). Impact of chicken litter pre-application treatment on the abundance, field persistence, and transfer of antibiotic resistant bacteria and antibiotic resistance genes to vegetables. Science of The Total Environment, 801, 149718. https://doi.org/10.1016/j.scitotenv.2021.149718

Taggar, G., Attiq Rehman, M., Boerlin, P., & Diarra, M. (2020). Molecular Epidemiology of Carbapenemases in Enterobacteriales from Humans, Animals, Food and the Environment. Antibiotics, 9(10), 693. https://doi.org/10.3390/antibiotics9100693

Tran, T. T., Scott, A., Tien, Y.-C., Murray, R., Boerlin, P., Pearl, D. L., Liu, K., Robertson, J., Nash, J. H. E., & Topp, E. (2021). On-Farm Anaerobic Digestion of Dairy Manure Reduces the Abundance of Antibiotic Resistance-Associated Gene Targets and the Potential for Plasmid Transfer. Applied and Environmental Microbiology, 87(14), e02980-20. https://doi.org/10.1128/AEM.02980-20

Turcotte, C., Thibodeau, A., Quessy, S., Topp, E., Beauchamp, G., Fravalo, P., Archambault, M., & Gaucher, M.-L. (2020). Impacts of Short-Term Antibiotic Withdrawal and Long-Term Judicious Antibiotic Use on Resistance Gene Abundance and Cecal Microbiota Composition on Commercial Broiler Chicken Farms in Québec. Frontiers in Veterinary Science, 7, 547181. https://doi.org/10.3389/fvets.2020.547181

Tymensen, L., Booker, C. W., Hannon, S. J., Cook, S. R., Jokinen, C. C., Zaheer, R., Read, R., Boerlin, P., & McAllister, T. A. (2019). Plasmid Distribution among Escherichia coli from Livestock and Associated Wastewater: Unraveling Factors That Shape the Presence of Genes Conferring Third-Generation Cephalosporin Resistance. Environmental Science & Technology, 53(20), 11666–11674. https://doi.org/10.1021/acs.est.9b03486

Xu, Q., Si, W., Mba, O. I., Sienkiewicz, O., Ngadi, M., Ross, K., Kithama, M., Kiarie, E. G., Kennes, Y.-M., Diarra, M. S., & Zhao, X. (2021). Research Note: Effects of supplementing cranberry and blueberry pomaces on meat quality and antioxidative capacity in broilers. Poultry Science, 100(3), 100900. https://doi.org/10.1016/j.psj.2020.11.069

Yang, C., Diarra, M. S., Choi, J., Rodas-Gonzalez, A., Lepp, D., Liu, S., Lu, P., Mogire, M., Gong, J., Wang, Q., & Yang, C. (2021). Effects of encapsulated cinnamaldehyde on growth performance, intestinal digestive and absorptive functions, meat quality and gut microbiota in broiler chickens. Translational Animal Science, 5(3), txab099. https://doi.org/10.1093/tas/txab099

Yang, C., Kennes, Y. M., Lepp, D., Yin, X., Wang, Q., Yu, H., Yang, C., Gong, J., & Diarra, M. S. (2020). Effects of encapsulated cinnamaldehyde and citral on the performance and cecal microbiota of broilers vaccinated or not vaccinated against coccidiosis. Poultry Science, 99(2), 936–948. https://doi.org/10.1016/j.psj.2019.10.036

Yang, C., Rehman, M. A., Yin, X., Carrillo, C. D., Wang, Q., Yang, C., Gong, J., & Diarra, M. S. (2021). Antimicrobial Resistance Phenotypes and Genotypes of Escherichia coli Isolates from Broiler Chickens Fed Encapsulated Cinnamaldehyde and Citral. Journal of Food Protection, 84(8), 1385–1399. https://doi.org/10.4315/JFP-21-033

Yousfi, K., Usongo, V., Berry, C., Khan, R. H., Tremblay, D. M., Moineau, S., Mulvey, M. R., Doualla-Bell, F., Fournier, E., Nadon, C., Goodridge, L., & Bekal, S. (2020). Source Tracking Based on Core Genome SNV and CRISPR Typing of Salmonella enterica Serovar Heidelberg Isolates Involved in Foodborne Outbreaks in Québec, 2012. Frontiers in Microbiology, 11, 1317. https://doi.org/10.3389/fmicb.2020.01317

Zaheer, R., Cook, S. R., Barbieri, R., Goji, N., Cameron, A., Petkau, A., Polo, R. O., Tymensen, L., Stamm, C., Song, J., Hannon, S., Jones, T., Church, D., Booker, C. W., Amoako, K., Van Domselaar, G., Read, R. R., & McAllister, T. A. (2020). Surveillance of Enterococcus spp. Reveals distinct species and antimicrobial resistance diversity across a One-Health continuum. Scientific Reports, 10(1), 3937. https://doi.org/10.1038/s41598-020-61002-5

Zaheer, R., Lakin, S. M., Polo, R. O., Cook, S. R., Larney, F. J., Morley, P. S., Booker, C. W., Hannon, S. J., Van Domselaar, G., Read, R. R., & McAllister, T. A. (2019). Comparative diversity of microbiomes and Resistomes in beef feedlots, downstream environments and urban sewage influent. BMC Microbiology, 19(1), 197. https://doi.org/10.1186/s12866-019-1548-x

Zaidi, S.-Z., Zaheer, R., Barbieri, R., Cook, S. R., Hannon, S. J., Booker, C. W., Church, D., Van Domselaar, G., Zovoilis, A., & McAllister, T. A. (2022). Genomic Characterization of Enterococcus hirae From Beef Cattle Feedlots and Associated Environmental Continuum. Frontiers in Microbiology, 13, 859990. https://doi.org/10.3389/fmicb.2022.859990

Zhang, A.-N., Gaston, J. M., Dai, C. L., Zhao, S., Poyet, M., Groussin, M., Yin, X., Li, L.-G., Van Loosdrecht, M. C. M., Topp, E., Gillings, M. R., Hanage, W. P., Tiedje, J. M., Moniz, K., Alm, E. J., & Zhang, T. (2021). An omics-based framework for assessing the health risk of antimicrobial resistance genes. Nature Communications, 12(1), 4765. https://doi.org/10.1038/s41467-021-25096-3

Zhang, H., Yamamoto, E., Murphy, J., Carrillo, C., & Locas, A. (2021). Shiga Toxin–Producing Escherichia coli (STEC) and STEC-Associated Virulence Genes in Raw Ground Pork in Canada. Journal of Food Protection, 84(11), 1956–1964. https://doi.org/10.4315/JFP-21-147

Zhang, L., Ben Said, L., Diarra, M. S., & Fliss, I. (2021). Inhibitory Activity of Natural Synergetic Antimicrobial Consortia Against Salmonella enterica on Broiler Chicken Carcasses. Frontiers in Microbiology, 12, 656956. https://doi.org/10.3389/fmicb.2021.656956

Zhang, T., Fukuda, K., Topp, E., Zhu, Y.-G., Smalla, K., Tiedje, J. M., & Larsson, D. G. J. (2020). Editorial: The Environmental Dimension of Antibiotic Resistance. FEMS Microbiology Ecology, 96(8), fiaa130. https://doi.org/10.1093/femsec/fiaa130

GRDI-AMR2

Brown, L. P., Murray, R., Scott, A., Tien, Y.-C., Lau, C. H.-F., Tai, V., & Topp, E. (2022). Responses of the Soil Bacterial Community, Resistome, and Mobilome to a Decade of Annual Exposure to Macrolide Antibiotics. Applied and Environmental Microbiology, 88(8), e00316-22. https://doi.org/10.1128/aem.00316-22

Cooper, A. L., Wong, A., Tamber, S., Blais, B. W., & Carrillo, C. D. (2024). Analysis of Antimicrobial Resistance in Bacterial Pathogens Recovered from Food and Human Sources: Insights from 639,087 Bacterial Whole-Genome Sequences in the NCBI Pathogen Detection Database. Microorganisms, 12(4), 709. https://doi.org/10.3390/microorganisms12040709

Darria, M. S., Zhao, X., & Butaye, P. (2023). Editorial: Antimicrobial use, antimicrobial resistance, and the microbiome in animals, volume II. Frontiers in Veterinary Science, 10, 1149010. https://doi.org/10.3389/fvets.2023.1149010

Das, Q., Hasted, T.-L., Lepp, D., Yin, X., Tang, J., Chalmers, G., Ross, K., Boerlin, P., & Diarra, M. S. (2023). Transcriptional profiling of extraintestinal Escherichia coli exposed to cranberry pomace extracts alone or in combination with ceftriaxone. Frontiers in Sustainable Food Systems, 6, 957099. https://doi.org/10.3389/fsufs.2022.957099

Demars, M., McDowell, T., Renaud, J. B., Scott, A., Fruci, M., & Topp, E. (2024). Persistence and evidence for accelerated biodegradation of streptomycin in agricultural soils. Science of The Total Environment, 929, 172502. https://doi.org/10.1016/j.scitotenv.2024.172502

Flint, A., Cooper, A., Rao, M., Weedmark, K., Carrillo, C., & Tamber, S. (2023). Targeted metagenomics using bait-capture to detect antibiotic resistance genes in retail meat and seafood. Frontiers in Microbiology, 14, 1188872. https://doi.org/10.3389/fmicb.2023.1188872

Flint, A., Laidlaw, A., Li, L., Raitt, C., Rao, M., Cooper, A., Weedmark, K., Carrillo, C., & Tamber, S. (2022). Choice of DNA extraction method affects detection of bacterial taxa from retail chicken breast. BMC Microbiology, 22(1), 230. https://doi.org/10.1186/s12866-022-02650-7

Flores-Vargas, G., Korber, D. R., & Bergsveinson, J. (2023). Sub-MIC antibiotics influence the microbiome, resistome and structure of riverine biofilm communities. Frontiers in Microbiology, 14, 1194952. https://doi.org/10.3389/fmicb.2023.1194952

George, P. B. L., Rossi, F., St-Germain, M.-W., Amato, P., Badard, T., Bergeron, M. G., Boissinot, M., Charette, S. J., Coleman, B. L., Corbeil, J., Culley, A. I., Gaucher, M.-L., Girard, M., Godbout, S., Kirychuk, S. P., Marette, A., McGeer, A., O’Shaughnessy, P. T., Parmley, E. J., … Duchaine, C. (2022). Antimicrobial Resistance in the Environment: Towards Elucidating the Roles of Bioaerosols in Transmission and Detection of Antibacterial Resistance Genes. Antibiotics, 11(7), 974. https://doi.org/10.3390/antibiotics11070974

Hetman, B. M., Pearl, D. L., Barker, D. O. R., Robertson, J., Nash, J. H. E., Reid-Smith, R., Agunos, A., Carrillo, C., Topp, E., Van Domselaar, G., Parmley, E. J., Bharat, A., Mulvey, M., Allen, V., & Taboada, E. N. (2022). Combining analytical epidemiology and genomic surveillance to identify risk factors associated with the spread of antimicrobial resistance in Salmonella enterica subsp. Enterica serovar Heidelberg. Microbial Genomics, 8(11). https://doi.org/10.1099/mgen.0.000891

Isada, M. J., Reist, M., MacKinnon, M. C., Uhland, F. C., Young, K. M., Gibbens, K., Parmley, E. J., & Carson, C. A. (2022). Characterisation of burden of illness measures associated with human (Fluoro)quinolone-resistant Campylobacter spp. Infections – a scoping review. Epidemiology and Infection, 150, e205. https://doi.org/10.1017/S095026882200139X

Johnson, L. A., Dufour, S. C., Smith, D. D. N., Manning, A. J., Ahmed, B., Binette, S., & Hamoutene, D. (2023). Descriptive analyses of bacterial communities in marine sediment microcosms spiked with fish wastes, emamectin benzoate, and oxytetracycline. Ecotoxicology and Environmental Safety, 268, 115683. https://doi.org/10.1016/j.ecoenv.2023.115683

Jonah, L., Hamoutene, D., Kingsbury, M., Johnson, L., & Fenton, A. J. (2024). A data compilation of antibiotic treatments in Canadian finfish aquaculture from 2016 to 2021 and the cumulative usage of antibiotics and antiparasitic drugs at marine sites. Environmental Reviews, er-2023-0124. https://doi.org/10.1139/er-2023-0124

Kang, H., Wang, Q., Yu, H., Guo, Q., Weber, Li., Wu, W., Lepp, D., Cui, S. W., Diarra, M. S., Liu, H., Shao, S., & Gong, J. (2024). Validating the use of a newly developed cinnamaldehyde product in commercial broiler production. Poultry Science, 103(5), 103625. https://doi.org/10.1016/j.psj.2024.103625

Kang, M., Charron, P., Hoover, E., Guan, J., Firth, I., Naushad, S., & Huang, H. (2023). Complete Genome Sequence of a Canadian Strain of Escherichia coli with Multiple Metal and Antimicrobial Resistance Genes That Was Isolated from Municipal Biosolids. Microbiology Resource Announcements, 12(5), e00083-23. https://doi.org/10.1128/mra.00083-23

Kang, M., Charron, P., Hoover, E., & Huang, H. (2024). Complete genome sequences of a Canadian strain of enteroaggregative Escherichia coli (EAEC) with multiple metals and antimicrobial resistance genes isolated from municipal waste-activated sludge. Microbiology Resource Announcements, 13(3), e01242-23. https://doi.org/10.1128/mra.01242-23

Kang, M., Naushad, S., Hartke, A., Firth, I., Madey, E., Ogunremi, D., & Huang, H. (2022). Antibiotic resistomes and microbial communities in biosolid fertilizers collected from two Canadian wastewater treatment plants in a 10-years interval-potential risks to food chains? Frontiers in Food Science and Technology, 2, 894671. https://doi.org/10.3389/frfst.2022.894671

Kleinman, D. R., Mitchell, R., McCracken, M., Hota, S. S., Golding, G. R., CNISP VRE Working Group, & Smith, S. W. (2023). Vancomycin-resistant Enterococcus sequence type 1478 spread across hospitals participating in the Canadian Nosocomial Infection Surveillance Program from 2013 to 2018. Infection Control & Hospital Epidemiology, 44(1), 17–23. https://doi.org/10.1017/ice.2022.7

Kujat Choy, S., Neumann, E.-M., Romero-Barrios, P., & Tamber, S. (2024). Contribution of Food to the Human Health Burden of Antimicrobial Resistance. Foodborne Pathogens and Disease, 21(2), 71–82. https://doi.org/10.1089/fpd.2023.0099

Lau, C. H.-F., Capitani, S., Tien, Y.-C., Verellen, L. A., Kithama, M., Kang, H., Kiarie, E. G., Topp, E., Diarra, M. S., & Fruci, M. (2024). Dynamic effects of black soldier fly larvae meal on the cecal bacterial microbiota and prevalence of selected antimicrobial resistant determinants in broiler chickens. Animal Microbiome, 6(1), 6. https://doi.org/10.1186/s42523-024-00293-9

Lee, C., Polo, R. O., Zaheer, R., Van Domselaar, G., Zovoilis, A., & McAllister, T. A. (2023). Evaluation of metagenomic assembly methods for the detection and characterization of antimicrobial resistance determinants and associated mobilizable elements. Journal of Microbiological Methods, 213, 106815. https://doi.org/10.1016/j.mimet.2023.106815

Lee, C., Zaheer, R., Munns, K., Holman, D. B., Van Domselaar, G., Zovoilis, A., & McAllister, T. A. (2023). Effect of Antimicrobial Use in Conventional Versus Natural Cattle Feedlots on the Microbiome and Resistome. Microorganisms, 11(12), 2982. https://doi.org/10.3390/microorganisms11122982

Liu, X. (Christine), Floate, K. D., Gorzelak, M. A., Holman, D. B., Hrycauk, S., Kubota, H., Lupwayi, N., Neilson, J. A. D., Ortega Polo, R., Petri, R. M., Tran, L., Wang, H., Wilches, D., Yang, X., Zorz, J., & Guarna, M. M. (2023). Prairie Agroecosystems: Interconnected Microbiomes of Livestock, Soil and Insects. Agriculture, 13(2), 326. https://doi.org/10.3390/agriculture13020326

Loest, D., Uhland, F. C., Young, K. M., Li, X.-Z., Mulvey, M. R., Reid-Smith, R., Sherk, L. M., & Carson, C. A. (2022). Carbapenem-resistant Escherichia coli from shrimp and salmon available for purchase by consumers in Canada: A risk profile using the Codex framework. Epidemiology and Infection, 150, e148. https://doi.org/10.1017/S0950268822001030

Mak, P. H. W., Rehman, M. A., Kiarie, E. G., Topp, E., & Diarra, M. S. (2022). Production systems and important antimicrobial resistant-pathogenic bacteria in poultry: A review. Journal of Animal Science and Biotechnology, 13(1), 148. https://doi.org/10.1186/s40104-022-00786-0

McMahon, T. C., Kingombe, C. B., Mathews, A., Seyer, K., Wong, A., Blais, B. W., & Carrillo, C. D. (2022). Microbial Antagonism in Food-Enrichment Culture: Inhibition of Shiga Toxin-Producing Escherichia coli and Shigella Species. Frontiers in Microbiology, 13, 880043. https://doi.org/10.3389/fmicb.2022.880043

Muhammad, B., Diarra, M. S., Islam, M. R., Lepp, D., Mastin-Wood, R. E., Topp, E., Bittman, S., & Zhao, X. (2022). Effects of litter from antimicrobial-fed broiler chickens on soil bacterial community structure and diversity. Canadian Journal of Microbiology, 68(10), 643–653. https://doi.org/10.1139/cjm-2022-0086

Phillips, C., Chapman, B., Agunos, A., Carson, C. A., Parmley, E. J., Reid-Smith, R. J., Smith, B. A., & Murphy, C. P. (2022). A scoping review of factors potentially linked with antimicrobial-resistant bacteria from turkeys (iAM.AMR Project). Epidemiology and Infection, 150, e153. https://doi.org/10.1017/S0950268822001224

Primeau, C. A., Bharat, A., Janecko, N., Carson, C. A., Mulvey, M., Reid-Smith, R., McEwen, S., McWhirter, J. E., & Parmley, E. J. (2023). Integrated surveillance of extended-spectrum beta-lactamase (ESBL)-producing Salmonella and Escherichia coli from humans and animal species raised for human consumption in Canada from 2012 to 2017. Epidemiology and Infection, 151, e14. https://doi.org/10.1017/S0950268822001509

Robertson, J., Schonfeld, J., Bessonov, K., Bastedo, P., & Nash, J. H. E. (2023). A global survey of Salmonella plasmids and their associations with antimicrobial resistance. Microbial Genomics, 9(5). https://doi.org/10.1099/mgen.0.001002

Shay, J. A., Haniford, L. S. E., Cooper, A., Carrillo, C. D., Blais, B. W., & Lau, C. H.-F. (2023). Exploiting a targeted resistome sequencing approach in assessing antimicrobial resistance in retail foods. Environmental Microbiome, 18(1), 25. https://doi.org/10.1186/s40793-023-00482-0

Strong, K. M., Marasco, K. L., Invik, J., Ganshorn, H., Reid-Smith, R. J., Waldner, C. L., Otto, S. J. G., Kastelic, J. P., & Checkley, S. L. (2023). Factors associated with antimicrobial resistant enterococci in Canadian beef cattle: A scoping review. Frontiers in Veterinary Science, 10, 1155772. https://doi.org/10.3389/fvets.2023.1155772

Subirats, J., Sharpe, H., Santoro, D., & Topp, E. (2023). Modeling Antibiotic Concentrations in the Vicinity of Antibiotic-Producing Bacteria at the Micron Scale. Applied and Environmental Microbiology, 89(4), e00261-23. https://doi.org/10.1128/aem.00261-23

Subirats, J., Sharpe, H., Tai, V., Fruci, M., & Topp, E. (2023). Metagenome meta-analysis reveals an increase in the abundance of some multidrug efflux pumps and mobile genetic elements in chemically polluted environments. Applied and Environmental Microbiology, 89(10), e01047-23. https://doi.org/10.1128/aem.01047-23

Subirats, J., Sharpe, H., & Topp, E. (2022). Fate of Clostridia and other spore-forming Firmicute bacteria during feedstock anaerobic digestion and aerobic composting. Journal of Environmental Management, 309, 114643. https://doi.org/10.1016/j.jenvman.2022.114643

Tan, D. T., Mulvey, M. R., Zhanel, G. G., Bay, D. C., Reid-Smith, R. J., Janecko, N., & Golding, G. R. (2022). A Clostridioides difficile surveillance study of Canadian retail meat samples from 2016-2018. Anaerobe, 74, 102551. https://doi.org/10.1016/j.anaerobe.2022.102551

Tapp, K., Deschênes, M., Cooper, A., Carrillo, C., & Blais, B. (2023). Genomically Informed Custom Selective Enrichment of Shiga Toxigenic Escherichia coli (STEC) Outbreak Strains in Foods Using Antibiotics. Journal of Food Protection, 86(3), 100052. https://doi.org/10.1016/j.jfp.2023.100052

Tisza, M. J., Smith, D. D. N., Clark, A. E., Youn, J.-H., NISC Comparative Sequencing Program, Barnabas, B. B., Black, S., Bouffard, G. G., Brooks, S. Y., Crawford, J., Marfani, H., Dekhtyar, L., Han, J., Ho, S.-L., Legaspi, R., Maduro, Q. L., Masiello, C. A., McDowell, J. C., Montemayor, C., … Dekker, J. P. (2023). Roving methyltransferases generate a mosaic epigenetic landscape and influence evolution in Bacteroides fragilis group. Nature Communications, 14(1), 4082. https://doi.org/10.1038/s41467-023-39892-6

VanderBurgt, J. T., Harper, O., Garnham, C. P., Kohalmi, S. E., & Menassa, R. (2023). Plant production of a virus-like particle-based vaccine candidate against porcine reproductive and respiratory syndrome. Frontiers in Plant Science, 14, 1044675. https://doi.org/10.3389/fpls.2023.1044675

Venkatesan, M., Fruci, M., Verellen, L. A., Skarina, T., Mesa, N., Flick, R., Pham, C., Mahadevan, R., Stogios, P. J., & Savchenko, A. (2023). Molecular mechanism of plasmid-borne resistance to sulfonamide antibiotics. Nature Communications, 14(1), 4031. https://doi.org/10.1038/s41467-023-39778-7

Yang, C., Das, Q., Rehman, M. A., Yin, X., Shay, J., Gauthier, M., Lau, C. H.-F., Ross, K., & Diarra, M. S. (2023). Microbiome of Ceca from Broiler Chicken Vaccinated or Not against Coccidiosis and Fed Berry Pomaces. Microorganisms, 11(5), 1184. https://doi.org/10.3390/microorganisms11051184

Yang, C., Diarra, M. S., Attiq Rehman, M., Li, L., Yu, H., Yin, X., Aslam, M., Carrillo, C. D., Yang, C., & Gong, J. (2023). Virulence potential of antimicrobial-resistant extraintestinal pathogenic Escherichia coli from retail poultry meat in a Caenorhabditis elegans model. Journal of Food Protection, 86(1), 100008. https://doi.org/10.1016/j.jfp.2022.11.001

Young, K. M., Isada, M. J., Reist, M., Uhland, F. C., Sherk, L. M., & Carson, C. A. (2023). A scoping review of the distribution and frequency of extended-spectrum β -lactamase (ESBL)-producing Enterobacteriaceae in shrimp and salmon. Epidemiology and Infection, 151, e1. https://doi.org/10.1017/S0950268822001819

Zaidi, S.-Z., Zaheer, R., Poulin-Laprade, D., Scott, A., Rehman, M. A., Diarra, M., Topp, E., Domselaar, G. V., Zovoilis, A., & McAllister, T. A. (2023). Comparative Genomic Analysis of Enterococci across Sectors of the One Health Continuum. Microorganisms, 11(3), 727. https://doi.org/10.3390/microorganisms11030727

Zaidi, S.-Z., Zaheer, R., Thomas, K., Abeysekara, S., Haight, T., Saville, L., Stuart-Edwards, M., Zovoilis, A., & McAllister, T. A. (2023). Genomic Characterization of Carbapenem-Resistant Bacteria from Beef Cattle Feedlots. Antibiotics, 12(6), 960. https://doi.org/10.3390/antibiotics12060960

Zhang, L., Ben Said, L., Diarra, M. S., & Fliss, I. (2022). Effects of bacterial-derived antimicrobial solutions on shelf-life, microbiota and sensory attributes of raw chicken legs under refrigerated storage condition. International Journal of Food Microbiology, 383, 109958. https://doi.org/10.1016/j.ijfoodmicro.2022.109958

Zhang, L., Ben Said, L., Hervé, N., Zirah, S., Diarra, M. S., & Fliss, I. (2022). Effects of drinking water supplementation with Lactobacillus reuteri, and a mixture of reuterin and microcin J25 on the growth performance, caecal microbiota and selected metabolites of broiler chickens. Journal of Animal Science and Biotechnology, 13(1), 34. https://doi.org/10.1186/s40104-022-00683-6

Publication library

GRDI-AMR1

GRDI-AMR2

See also